comparison trim_galore.xml @ 11:80cd83b11214 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf

10:b4e39d993fc8

<tool id="trim_galore" name="Trim Galore!" version="0.4.3" profile="17.01">
    <!-- Wrapper compatible with Trim Galore! version 0.4 -->
    <description>Quality and adapter trimmer of reads</description>
    <macros>
        <macro name="adapter_trimming">
            <conditional name="trimming">
                <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">

                    <yield/>
                </when>
            </conditional>
        </macro>
        <macro name="paired_adapter_trimming">

            <expand macro="adapter_trimming">
                <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
                    <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
                </param>
            </expand>

                    the 3' end that is not directly related to adapter sequence or basecall quality.</help>
            </param>
        </macro>
    </macros>
    <requirements>
        <!-- conda dependency -->
        <requirement type="package" version="1.8.3">cutadapt</requirement>
        <requirement type="package" version="1.8">cutadapt</requirement>
    </requirements>
    <version_command>
        perl '$__tool_directory__/trim_galore' --version
    </version_command>
    <command>
<![CDATA[

        #set compressed = 'no'
        #if $singlePaired.sPaired == "single":
            #if $singlePaired.input_singles.is_of_type("fastq.gz"):
                #set read1 = 'input_1.fastq.gz'
                #set compressed = 'gz'

                #set read2 = 'input_2.fastq'
            #end if
            ln -s '${singlePaired.input_mate_pairs.reverse}' ${read2} &&
        #end if

        perl '$__tool_directory__/trim_galore'

        ## we only support fastqsanger
        --phred33

        #if $params.settingsType == "custom":

        #end if

        #if $singlePaired.trimming.trimming_select == 'user':
            ## default 'AGATCGGAAGAGC'
            #if $singlePaired.trimming.adapter.strip() != '':
               --adapter $singlePaired.trimming.adapter
            #end if
        #else:
            $singlePaired.trimming.trimming_select
        #end if


        #if $singlePaired.three_prime_clip_R1:
            --three_prime_clip_R1 $singlePaired.three_prime_clip_R1
        #end if

            $singlePaired.trim1

            #if $singlePaired.trimming.trimming_select == 'user':
                #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '':
                    --adapter2 $singlePaired.trimming.adapter2
                #end if
            #end if

            #if $singlePaired.three_prime_clip_R2:
                --three_prime_clip_R2 $singlePaired.three_prime_clip_R2

        if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi

        ##  Trim Galore! run is finished. Move the report files to the proper place
        #if $params.settingsType == "custom" and $params.report:
            &&
            cat ./*_trimming_report.txt > $report_file;
        #end if

]]>
    </command>
    <inputs>
        <!-- Input Parameters -->
        <conditional name="singlePaired">
            <param name="sPaired" type="select" label="Is this library paired- or single-end?">
                <option value="single">Single-end</option>

                    label="Specifies that the input file was an MspI digested RRBS sample" />
                <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False"
                    label="Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs" />
            </when>  <!-- full -->
        </conditional>  <!-- params -->

    </inputs>
    <outputs>
        <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
            <filter>singlePaired['sPaired'] == "single"</filter>
        </data>

        </data>
        <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file">
            <filter>params['settingsType'] == "custom"</filter>
            <filter>params['report'] == True</filter>
        </data>

    </outputs>
    <tests>
        <test>
            <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
            <param name="sPaired" value="single" />
            <param name="settingsType" value="custom" />

                <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
                <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
            </output_collection>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

`Trim Galore!`_ is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are:

 * For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too

**Main Settings**

* **Adapter sequence to be trimmed**

  * **Automatic detection**
    
      | Adapter sequence to be trimmed. Trim Galore will try to auto-detect whether the Illumina universal, Nextera transposase or Illumina small RNA adapter sequence was used.

  * **Illumina universal**

      | Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter 'AGATCGGAAGAGC' instead of the default auto-detection of adapter sequence.

      |
      |   R1 --------------------------->
      |   R2 <---------------------------
      |
      | or this:
      | 
      |   R1 ----------------------->
      |   R2 <-----------------
      |
      | as invalid (whenever a start/end coordinate is contained within the other read).
      |

* **Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs**

    | Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs. Like with the option '--rrbs' this avoids using cytosine positions that were filled-in during the end-repair step. '--non_directional' requires '--rrbs' to be specified as well.
    |
    | *option --non_directional*]]>
    </help>
    <citations></citations>
</tool>

11:80cd83b11214

<tool id="trim_galore" name="Trim Galore!" version="0.4.3.0" profile="17.01">
    <!-- Wrapper compatible with Trim Galore! version 0.4.3 -->
    <description>Quality and adapter trimmer of reads</description>
    <macros>
        <macro name="adapter_trimming">
            <conditional name="trimming">
                <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">

                    <yield/>
                </when>
            </conditional>
        </macro>
        <macro name="paired_adapter_trimming">
            <expand macro="adapter_trimming">
                <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
                    <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
                </param>
            </expand>

                    the 3' end that is not directly related to adapter sequence or basecall quality.</help>
            </param>
        </macro>
    </macros>
    <requirements>
        <requirement type="package" version="0.4.3">trim-galore</requirement>
    </requirements>
    <version_command>
        trim_galore --version
    </version_command>
    <command><![CDATA[
        #set compressed = 'no'
        #if $singlePaired.sPaired == "single":
            #if $singlePaired.input_singles.is_of_type("fastq.gz"):
                #set read1 = 'input_1.fastq.gz'
                #set compressed = 'gz'

                #set read2 = 'input_2.fastq'
            #end if
            ln -s '${singlePaired.input_mate_pairs.reverse}' ${read2} &&
        #end if

        trim_galore

        ## we only support fastqsanger
        --phred33

        #if $params.settingsType == "custom":

        #end if

        #if $singlePaired.trimming.trimming_select == 'user':
            ## default 'AGATCGGAAGAGC'
            #if $singlePaired.trimming.adapter.strip() != '':
               --adapter '$singlePaired.trimming.adapter'
            #end if
        #else:
            $singlePaired.trimming.trimming_select
        #end if

        #if $singlePaired.three_prime_clip_R1:
            --three_prime_clip_R1 $singlePaired.three_prime_clip_R1
        #end if

            $singlePaired.trim1

            #if $singlePaired.trimming.trimming_select == 'user':
                #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '':
                    --adapter2 '$singlePaired.trimming.adapter2'
                #end if
            #end if

            #if $singlePaired.three_prime_clip_R2:
                --three_prime_clip_R2 $singlePaired.three_prime_clip_R2

        if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi

        ##  Trim Galore! run is finished. Move the report files to the proper place
        #if $params.settingsType == "custom" and $params.report:
            &&
            cat ./*_trimming_report.txt > '$report_file'
        #end if
    ]]></command>
    <inputs>
        <!-- Input Parameters -->
        <conditional name="singlePaired">
            <param name="sPaired" type="select" label="Is this library paired- or single-end?">
                <option value="single">Single-end</option>

                    label="Specifies that the input file was an MspI digested RRBS sample" />
                <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False"
                    label="Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs" />
            </when>  <!-- full -->
        </conditional>  <!-- params -->
    </inputs>

    <outputs>
        <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
            <filter>singlePaired['sPaired'] == "single"</filter>
        </data>

        </data>
        <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file">
            <filter>params['settingsType'] == "custom"</filter>
            <filter>params['report'] == True</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
            <param name="sPaired" value="single" />
            <param name="settingsType" value="custom" />

                <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
                <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`Trim Galore!`_ is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are:

 * For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too

**Main Settings**

* **Adapter sequence to be trimmed**

  * **Automatic detection**

      | Adapter sequence to be trimmed. Trim Galore will try to auto-detect whether the Illumina universal, Nextera transposase or Illumina small RNA adapter sequence was used.

  * **Illumina universal**

      | Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter 'AGATCGGAAGAGC' instead of the default auto-detection of adapter sequence.

      |
      |   R1 --------------------------->
      |   R2 <---------------------------
      |
      | or this:
      |
      |   R1 ----------------------->
      |   R2 <-----------------
      |
      | as invalid (whenever a start/end coordinate is contained within the other read).
      |

* **Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs**

    | Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs. Like with the option '--rrbs' this avoids using cytosine positions that were filled-in during the end-repair step. '--non_directional' requires '--rrbs' to be specified as well.
    |
    | *option --non_directional*
    ]]></help>
    <citations></citations>
</tool>